Graham McVicker

Frederick B. Rentschler Developmental Chair
Assistant Professor
Laboratory of Genetics
Integrative Biology Laboratory

Salk Institute for Biological Studies - Publications

all Publications


Nott, A., Holtman, I.R., Coufal, N.G., Schlachetzki, J.C.M., Yu, M., Hu, R., Han, C.Z., Pena, M., Xiao, J., Wu, Y., Keulen, Z., Pasillas, M.P., O'Connor, C., Nickl, C.K., Schafer, S.T., Shen, Z., Rissman, R.A., Brewer, J.B., Gosselin, D., Gonda, D.D., Levy, M.L., Rosenfeld, M.G., McVicker, G., Gage, F.H., Ren, B., Glass, C.K. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. (2019) Science. DOI: 10.1126/science.aay0793

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Schmiedel, B.J., Singh, D., Madrigal, A., Valdovino-Gonzalez, A.G., White, B.M., Zapardiel-Gonzalo, J., Ha, B., Altay, G., Greenbaum, J.A., McVicker, G., Seumois, G., Rao, A., Kronenberg, M., Peters, B., Vijayanand, P. Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. (2018) Cell. DOI: 10.1016/j.cell.2018.10.022

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Martin, R.L., Maiorano, J., Beitel, G.J., Marko, J.F., McVicker, G., Fondufe-Mittendorf, Y.N. A comparison of nucleosome organization in Drosophila cell lines. (2017) PLOS One. 12(6):e0178590. DOI: 10.1371/journal.pone.0178590

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Elyashiv, E., Sattath, S., Hu, T.T., Strutsovsky, A., McVicker, G., Andolfatto, P., Coop, G., Sella, G. A Genomic Map of the Effects of Linked Selection in Drosophila. (2016) PLOS Genetics. 12(8):e1006130. DOI: 10.1371/journal.pgen.1006130

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van de Geijn, B.*, McVicker, G.*, Gilad, Y., Pritchard, J.K. WASP: allele-specific software for robust molecular quantitative trait locus discovery. (2015) Nature Methods. 12(11):1061-3. DOI: 10.1038/nmeth.3582

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Banovich, N.E., Lan, X., McVicker, G., van de Geijn, B., Degner, J.F., Blischak, J.D., Roux, J., Pritchard, J.K., Gilad, Y. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. (2014) PLOS Genetics. 10(9):e1004663. DOI: 10.1371/journal.pgen.1004663

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Nalabothula, N.*, McVicker, G.*, Maiorano, J., Martin, R., Pritchard, J.K., Fondufe-Mittendorf, Y.N. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. (2014) BMC Genomics. 15:92. DOI: 10.1186/1471-2164-15-92

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Raj, A., McVicker, G. The genome shows its sensitive side. (2014) Nature Methods. 11(1):39-40. DOI: 10.1038/nmeth.2770


McVicker, G.*, van de Geijn, B.*, Degner, J.F., Cain, C.E., Banovich, N.E., Raj, A., Lewellen, N., Myrthil, M., Gilad, Y., Pritchard, J.K. Identification of genetic variants that affect histone modifications in human cells. (2013) Science. 342(6159):747-9. DOI: 10.1126/science.1242429

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Gaffney, D.J.*, McVicker, G.*, Pai, A.A., Fondufe-Mittendorf, Y.N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y., Pritchard, J.K. Controls of nucleosome positioning in the human genome. (2012) PLOS Genetics. 8(11):e1003036. DOI: 10.1371/journal.pgen.1003036

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George, R.D., McVicker, G., Diederich, R., Ng, S.B., MacKenzie, A.P., Swanson, W.J., Shendure, J., Thomas, J.H. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. (2011) Genome Research. 21(10):1686-94. DOI: 10.1101/gr.121327.111

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D'Souza, C.A., Kronstad, J.W., Taylor, G., Warren, R., Yuen, M., Hu, G., Jung, W.H., Sham, A., Kidd, S.E., Tangen, K., Lee, N., Zeilmaker, T., Sawkins, J., McVicker, G., Shah, S., Gnerre, S., Griggs, A., Zeng, Q., Bartlett, K., Li, W., Wang, X., Heitman, J., Stajich, J.E., Fraser, J.A., Meyer, W., Carter, D., Schein, J., Krzywinski, M., Kwon-Chung, K.J., Varma, A., Wang, J., Brunham, R., Fyfe, M., Ouellette, B.F., Siddiqui, A., Marra, M., Jones, S., Holt, R., Birren, B.W., Galagan, J.E., Cuomo, C.A. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. (2011) MBio. 2(1):e00342-10. DOI: 10.1128/mBio.00342-10

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McVicker, G., Green, P. Genomic signatures of germline gene expression. (2010) Genome Research. 20(11):1503-11. DOI: 10.1101/gr.106666.110

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McVicker, G., Gordon, D., Davis, C., Green, P. Widespread genomic signatures of natural selection in hominid evolution. (2009) PLOS Genetics. 5(5):e1000471. DOI: 10.1371/journal.pgen.1000471

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Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, X.M., Gilbert, J., Hammond, M., Herrero, J., Hotz, H., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Kokocinsci, F., London, D., Longden, I., McVicker, G., Melsopp, C., Meidl, P., Potter, S., Proctor, G., Rae, M., Rios, D., Schuster, M., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C., Birney, E. Ensembl 2005. (2005) Nucleic Acids Research. 33(Database i):D447-53. DOI: 10.1093/nar/gki138

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Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., Birney, E. The Ensembl core software libraries. (2004) Genome Research. 14(5):929-33. DOI: 10.1101/gr.1857204

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Birney, E., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H.R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K.C., Cameron, G., Durbin, R., Cox, A., Hubbard, T., Clamp, M. An overview of Ensembl. (2004) Genome Research. 14(5):925-8. DOI: 10.1101/gr.1860604

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Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., Hubbard, T. Ensembl 2004. (2004) Nucleic Acids Research. 32(Database i):D468-70. DOI: 10.1093/nar/gkh038

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Shah, S.P., McVicker, G.P., Mackworth, A.K., Rogic, S., Ouellette, B.F. GeneComber: combining outputs of gene prediction programs for improved results. (2003) Bioinformatics . 19(10):1296-7.

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Education

BS, Computer Science, University of British Columbia
PhD, Genome Sciences, University of Washington


Awards & Honors

  • 2009 Society for Molecular Biology and Evolution Graduate Student Travel Award
  • 2005 Natural Science and Engineering Research Council Post Graduate Scholarship
  • 1997 University of British Columbia Outstanding Student Initiative Scholarship